Community manual annotation with Apollo (faqs)

How to upload BLAST hits to Apollo?

Answer: 
Run a BLAST job. In the results page for chromosomes, scaffolds, or contigs, click on 'GFF file for Apollo'. Save this file for later. Select the best hit In the pop-out window click on 'Browse Genome'

Automatic emails explained

Answer: 

Top tip: If you are splitting a gene model, you need to account for all children, tidy up after yourself!

Error in Gene Annotation

Q1. How to mark genes with no stop and/or no start codon?

Why don't you accept unmodified gene models?

Answer: 

We only use Apollo to receive your submissions of modification to gene structure, i.e., changes to the exon/

I just submitted my gene annotation. When will I see my submission incorporated in VectorBase?

Answer: 
  • VectorBase Apollo captures community gene annotations (i.e., corrections of gene structures) and other gene information such as metadata (for a few or group gene submissions), links your publications to the relevant gene(s) in the genome browser, allows gene deletions and repeat submissions too, follow this link for instructions.

How do I set a gene to pseudogene?

Answer: 

Use VectorBase web form called Gene Metadata following this link and select "

How do I decide on a gene name (symbol)?

Answer: 

  • Gene names (symbols) are few letters (such as "W" for the white gene, "INR" for insulin receptor, "SRPN18" for serpin 18 in Anopheles) and should be unique for each gene.
  • Gene descriptions are the "spelt out" version of the name (symbol), so "white", "insulin receptor" or "serpin 18" respectively, and are also unique for each gene.

How do I annotate a gene?

Answer: 

Apollo working space has the "User-created annotation tracks" on top and, below that an area were you can add evidence tracks. Activate the gene set track. Select, hold and drag a partial or full

How do I batch submit annotation metadata to VectorBase?

Answer: 

If you are submitting in batch, e.g., when you are annotating a gene family, you can fill an spreadsheet (e.g., Excel), rather than the web form for one gene at the time. Once you are done please send the file to info@vectorbase.org. Use the following 12 columns headings in the spreadsheet:

How do I add a comment to a gene?

Answer: 

Please type your comments in the "Gene Metadata" web form following this link.

Annotation Editors: Artemis and Apollo

Answer: 

There are a few annotation editors including Apollo and Artemis. Currently we only support Apollo for the VectorBase genome communities, which is also the tool of choice of the i5k community.

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